Genomics and Applied Biology 2024, Vol.15, No.5, 245-254 http://bioscipublisher.com/index.php/gab 247 The phylogenetic analysis of Forficula auricularia (European earwig) conducted by Bhattarai et al. (2022b) reveals two major subspecies groups, which align with the findings of previous studies such as Wirth et al. (1998). One clade consists of 24 individuals, including subspecies A, while the second group, subspecies B, includes the genome analyzed in this study from Dunedin, New Zealand. By utilizing mitochondrial genes COI and COII, along with phylogenetic methods like Neighbour-Joining and Maximum Composite Likelihood, the study provides reliable evolutionary insights. It highlights the genetic diversity within F. auricularia populations across different geographic regions, reinforcing the subspecies differentiation. These findings underscore the importance of genomic resources in understanding earwig adaptation and contribute to broader discussions on insect evolution and local environmental pressures, especially in the case of subspecies B in New Zealand. 2.2 Challenges in earwig genome assembly One of the primary challenges in assembling the earwig genome is the high repeat content, which constitutes 64.62% of the genome. This high repeat content can complicate the assembly process, leading to potential gaps and misassemblies (Bhattarai et al., 2022a; 2022b). Additionally, the presence of extensive gene rearrangements, as observed in the mitochondrial genomes of Haplodiplatyidae, adds another layer of complexity to the assembly process (Liu et al., 2022). These rearrangements can result in difficulties in accurately annotating and aligning the genomic sequences. 2.3 Comparative analysis of earwig genomes with other insect species Comparative genomic analyses have revealed significant insights into the evolutionary adaptations of earwigs. For instance, the genome of Forficula auricularia has been compared with other insect genomes to identify unique and conserved genetic elements. The benchmarking of Universal Single-Copy Orthologs (BUSCO) scores, which are approximately 90% for eukaryotic, insect, and arthropod orthologs, indicates a high level of completeness and accuracy in the earwig genome assembly (Bhattarai et al., 2022a; 2022b). Furthermore, studies on other insect genomes, such as the spruce budworm (Choristoneura fumiferana) and the eastern fence lizard (Sceloporus undulatus), have provided valuable comparative data. For example, synteny analysis with the Bombyx mori genome revealed the presence of a neo-Z chromosome in the spruce budworm, highlighting the evolutionary dynamics of sex chromosomes in insects (Picq et al., 2018). Similarly, the high-quality chromosome-level genome assembly of the eastern fence lizard has facilitated synteny and whole-genome association mapping analyses, which can be applied to earwig genomic studies to understand chromosome evolution and adaptation mechanisms (Westfall et al., 2021). 3 Genomic Features of Earwigs 3.1 Gene family expansions and their functions Gene family expansions play a crucial role in the evolutionary adaptation of organisms to their environments. In the case of earwigs, the sequencing and analysis of their genomes have revealed significant gene rearrangements and expansions. For instance, the mitochondrial genomes of the earwig species Haplodiplatys aotouensis showed extensive gene rearrangement events, particularly in protein-coding genes (PCGs) and transfer RNA (tRNA) genes (Liu et al., 2022). These rearrangements and expansions are indicative of the evolutionary pressures and adaptations that earwigs have undergone. Moreover, gene family expansions have been observed in other species as a response to environmental pressures. For example, the pinewood nematode Bursaphelenchus xylophilus exhibited expansions in gene families associated with xenobiotic detoxification pathways, such as flavin monooxygenase (FMO) and cytochrome P450 (CYP450) (Zhang et al., 2020). These expansions likely facilitate the nematode's adaptation to its host's defense chemicals. Similarly, such expansions in earwigs could be linked to their unique ecological niches and survival strategies. 3.2 Identification of genes involved in environmental adaptation Identifying genes involved in environmental adaptation is essential for understanding how earwigs thrive in diverse habitats. Comparative genomic studies have highlighted the role of specific genes in adaptation to
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